Align ABC transporter permease (characterized, see rationale)
to candidate WP_027456720.1 K420_RS0102840 branched-chain amino acid ABC transporter permease
Query= uniprot:A0A165KC95 (309 letters) >NCBI__GCF_000519045.1:WP_027456720.1 Length = 307 Score = 353 bits (906), Expect = e-102 Identities = 181/310 (58%), Positives = 235/310 (75%), Gaps = 4/310 (1%) Query: 1 MDILLQQIINGLVLGSMYALIALGYTMVYGIIQLINFAHGEVLMIGALTSWSCIG-MMQG 59 MDI LQQI+NGLV GS+YAL+ALGYTMVYGI+ LINFAHGEV+MIG L + + G +++ Sbjct: 1 MDIFLQQIVNGLVQGSIYALVALGYTMVYGIMGLINFAHGEVVMIGTLVTITVAGSLIKA 60 Query: 60 AMPGAPGWVILLLATIIACVVAATLNFVIEKVAYRPLRSSPRLAPLITAIGMSILLQTLA 119 MP A + L +++ C+ L + +E++AYRPLR++PRL PLITAIGMSI+LQ LA Sbjct: 61 GMPVALAALAGLSVSLLLCMA---LGWGLERIAYRPLRNAPRLTPLITAIGMSIVLQNLA 117 Query: 120 MIIWKPNYKPYPTMLPSSPFEIGGAFITPTQILILGVTAVALASLVYLVNHTNLGRAMRA 179 M+IW NY +P +LP FE+ GA T Q++I+ ++ +A L+ L+ T LG AMRA Sbjct: 118 MMIWGRNYLTFPALLPKVNFELAGAHFTFIQVVIVLLSGATMAGLLGLIYRTKLGMAMRA 177 Query: 180 TAENPRVASLMGVKPDMVISATFIIGAVLAAIAGIMYASNYGTAQHTMGFLPGLKAFTAA 239 TA+NP VASLMGV + VI+A F+IG+ L A+AG+M + Y A + MGF+ GLKAFTAA Sbjct: 178 TAQNPAVASLMGVNINRVIAAAFVIGSALGALAGVMVGTYYEIAHYQMGFMLGLKAFTAA 237 Query: 240 VFGGIGNLAGAVVGGILLGLIEAIGSGYIGTLTGGLLGSHYTDIFAFIVLIIILTLRPSG 299 V GGIGNLAGA++GG+LLG+IEA+G+GYIG LTGG LGSHY DIFAFIVLI++L +PSG Sbjct: 238 VLGGIGNLAGAMLGGVLLGIIEALGAGYIGDLTGGFLGSHYQDIFAFIVLIVVLMFKPSG 297 Query: 300 LLGERVADRA 309 L GE+ DRA Sbjct: 298 LFGEKTGDRA 307 Lambda K H 0.327 0.142 0.419 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 286 Number of extensions: 15 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 309 Length of database: 307 Length adjustment: 27 Effective length of query: 282 Effective length of database: 280 Effective search space: 78960 Effective search space used: 78960 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.7 bits) S2: 48 (23.1 bits)
This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory